Hi all,
I ran the same job with pmemd instead of pmemd.CUDA and it worked just fine. Any suggestions how I could make it run on pmemd.CUDA?
-----Original Message-----
From: Andreas Tosstorff [mailto:andreas.tosstorff.cup.uni-muenchen.de]
Sent: Thursday, December 15, 2016 4:00 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] pmemd.cuda incomplete output file
Dear AMber users,
I have been running some MD simulations and I just realized that the equilibration runs are not being completed. Instead they appear to b just canceled without any warning or error.
nstlim is set to 250000, and the last print out is done for example at 105000.
Any idea what might be going wrong? The consecutive production run starts fine, but of course at different starting times depending on the length of the previous equilibration.
Here is the input file:
100 ps NPT equilibration for 40 A
Constant pressure constant temperature production run
&cntrl
nstlim=250000, dt=0.002, ntx=1, irest=0, ntpr=5000, ntwr=5000, ntwx=0,
tempi=0.0, temp0=300.0, ntt=3, gamma_ln=5.0, tautp=2.0, cut=8.,
ntb=2, ntp=1,
ntc=2, ntf=2, tol=0.000001,
nmropt = 1, ioutfm = 1,
&end
&ewald
dsum_tol=0.000001,
/
&wt
type='END',
&end
DISANG=disang.40
Note: ig = -1. Setting random seed to 918652 based on wallclock time in
microseconds.
-------------------------
The last print out reads this:
NSTEP = 105000 TIME(PS) = 210.000 TEMP(K) = 301.69 PRESS =
-51.2
Etot = -154333.0068 EKtot = 39629.2422 EPtot =
-193962.2490
BOND = 1286.3834 ANGLE = 3286.3140 DIHED = 5478.7889
1-4 NB = 1478.0926 1-4 EEL = 18800.2459 VDWAALS = 23333.4598
EELEC = -247625.5494 EHBOND = 0.0000 RESTRAINT =
0.0158
EAMBER (non-restraint) = -193962.2648
EKCMT = 17267.8494 VIRIAL = 17979.7511 VOLUME =
643904.2607
Density =
1.0187
------------------------------------------------------------------------------
NMR restraints: Bond = 0.016 Angle = 0.000 Torsion = 0.000
===============================================================================
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie Department Pharmazie LMU München Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Thu Dec 15 2016 - 14:00:02 PST
